AMBER Archive (2007)

Subject: Re: AMBER: divcon missing in Antechamber 1.27

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Mon May 28 2007 - 21:18:08 CDT

Hello,

I currently have amber7 available to me (which lacks divcon too) . But for
what I talk about below, I downloaded the standalone Antechamber 1.27, and I
made a 'hybrid' directory where I added to the /exe/ and /dat/, the stuff
from amber7 that were not present in Antechamber1.27. I just setenv
AMBERHOME as the path to this hybrid directory.
I know this is not elegant, but could you point out how to get a working
knowledge of Antechamber with what I have (is there a tutorial written with
amber7 in mind)? I am a new user of Amber, and I intend to simulate some
artificial peptides with non-standard capping groups.

Thanks,
Neelanjana

On 5/28/07, David A. Case <case_at_scripps.edu> wrote:
>
> On Mon, May 28, 2007, Neelanjana Sengupta wrote:
> >
> > I downloaded Antechamber Version 1.27 from the Amber website. It looks
> like
> > divcon is missing from this version... When I try Ross Walker's tutorial
> > with sustiva, ie. I type the command,
> >
> > $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo
> > prepi -c bcc -s 2
> >
> > I get this output:
> > ====================
> > Running: /w1/antech127/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
> > ANTECHAMBER_BOND_TYPE.AC -f ac -j full
> >
> > Running: /w1/antech127/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
> > ANTECHAMBER_AC.AC -p gaff
> >
> > Total number of electrons: 160; net charge: 0
> >
> > Running: $AMBERHOME/exe/divcon
> > sh: /w1/antech127/exe/divcon: No such file or directory
> > Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c properly,
> > exit
> > ====================
> > Please let me know what the issue is here...
> >
>
> You are mixing up the Amber version of antechamber and the "stand-alone"
> one.
> The version shipped with Amber runs from $AMBERHOME/exe and invokes divcon
> to do the semi-empirical calculations.
>
> The standalone version (from http://amber.scripps.edu/antechamber) does
> not require an Amber installation. It runs from $ACHOME/bin, and invokes
> mopac6 for the semiempirical calculations. See the documentation that
> comes
> with the antechamber tar file for installation instructions.
>
> There are plusses and minuses to each of these semi-empirical programs,
> but
> you have to choose one or the other. From your mail, it looks like you
> are
> running the Amber version(?). You don't say which release of Amber you
> are
> using, but an Amber 9 installation should have a divcon executable in
> $AMBERHOME/exe.
>
> Note also that the tutorial one the Amber web site refers to the Amber
> version. You will have to make (trivial) changes to use it with the
> stand-alone version (e.g. replace $AMBERHOME with $ACHOME).
>
> ...hope this helps....dac
>
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